DCI1 (YOR180C; also called ECI2/EHD2) encodes a peroxisomal protein of the enoyl-CoA hydratase/isomerase (crotonase) family, about 50% identical to the Delta(3)-Delta(2)-enoyl-CoA isomerase Eci1p, that was identified as a Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase (di-isomerase, EC 5.3.3.21). This identification is disputed: di-isomerase activity was measured in extracts of Dci1p-overproducing cells, but a later study found no activity in purified MBP-Dci1p and higher, not lower, di-isomerase activity in dci1 deletion cells. As proposed, Dci1p converts 3,5-dienoyl-CoAs, formed during beta-oxidation of unsaturated fatty acids with double bonds at odd-numbered positions, into 2,4-dienoyl-CoAs that are then reduced by 2,4-dienoyl-CoA reductase (Sps19p). Extracts of Dci1p-overproducing cells also show a weak intrinsic 3,2-isomerase activity, but genetic analysis indicates that Dci1p is not a physiological 3,2-isomerase: dci1 deletion mutants grow essentially normally on oleate, and the di-isomerase-dependent route is dispensable for oleate degradation, whereas Eci1p is essential. Dci1p is an oleate-induced (Oaf1/Pip2-regulated) peroxisomal matrix protein; it interacts with Eci1p and is needed for efficient peroxisomal import of Eci1p, which can enter peroxisomes using either its own PTS1 or that of Dci1p.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004165 delta(3)-delta(2)-enoyl-CoA isomerase activity | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA from the PANTHER enoyl-CoA isomerase node (PTN000234739) seeded by mammalian ECI1/ECI2 and yeast Eci1p and Dci1p. Dci1p extracts do carry a weak intrinsic Delta3-Delta2 isomerase activity, so the activity claim is not wrong, but Gurvitz et al. concluded that Dci1p is not a physiological 3,2-isomerase; its characteristic activity is the Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase reaction. Supporting Evidence: PMID:10455114 contained an intrinsic 3,2-isomerase activity that could generate 3, 5,8,11,14-eicosapentenoyl-CoA from 2,5,8,11,14-eicosapentenoyl-CoA but not metabolize trans-3-hexenoyl-CoA PMID:10455114 we reasoned that yeast di-isomerase does not additionally represent a physiological 3,2-isomerase |
| GO:0004165 delta(3)-delta(2)-enoyl-CoA isomerase activity | IDA PMID:10455114 Alternatives to the isomerase-dependent pathway for the beta... | KEEP AS NON CORE | Summary: IDA from Gurvitz et al. 1999: extracts of Dci1p-overproducing eci1-deleted cells converted 2,5,8,11,14-eicosapentenoyl-CoA to its 3-isomer, i.e. an intrinsic 3,2-isomerase activity, and amplifying it rescued eci1 growth on petroselinic acid. The activity is real in vitro but the same paper concludes it is not physiologically relevant, so it is kept as non-core. Supporting Evidence: PMID:10455114 contained an intrinsic 3,2-isomerase activity that could generate 3, 5,8,11,14-eicosapentenoyl-CoA from 2,5,8,11,14-eicosapentenoyl-CoA but not metabolize trans-3-hexenoyl-CoA PMID:10455114 we reasoned that yeast di-isomerase does not additionally represent a physiological 3,2-isomerase |
| GO:0004165 delta(3)-delta(2)-enoyl-CoA isomerase activity | RCA GO_REF:0000123 | MODIFY | Summary: YeastPathways (YEAST-FAO-PWY) assigns Dci1p to the Delta3-Delta2-enoyl-CoA isomerase step (EC 5.3.3.8) of fatty acid oxidation, the step catalysed by Eci1p. The direct evidence shows Dci1p is the Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase (EC 5.3.3.21) and is not a physiological 3,2-isomerase; the pathway assignment should point to the di-isomerase activity. Proposed replacements: delta(3,5)-delta(2,4)-dienoyl-CoA isomerase activity Supporting Evidence: PMID:10455114 Enzyme assays conducted on soluble extracts derived from yeast cells overproducing Dci1p using 3,5,8,11,14-eicosapentenoyl-CoA as substrate demonstrated a specific di-isomerase activity of 6 nmol x min(-1) per mg of protein PMID:10455114 we reasoned that yeast di-isomerase does not additionally represent a physiological 3,2-isomerase |
| GO:0005737 cytoplasm | HDA PMID:24390141 A visual screen of protein localization during sporulation i... | TOO GENERAL | Summary: HDA from a GFP-fusion screen of protein localization during sporulation (Lam et al. 2014). Cytoplasm is a broad parent that includes peroxisomes; well-supported direct data place Dci1p in the peroxisomal matrix. Not wrong, but uninformative. Supporting Evidence: file:yeast/DCI1/DCI1-uniprot.txt SUBCELLULAR LOCATION: Peroxisome |
| GO:0005777 peroxisome | EXP PMID:10381339 Preliminary characterization of Yor180Cp: identification of ... | ACCEPT | Summary: Geisbrecht et al. 1999 showed that Yor180Cp/Dci1p targets GFP to peroxisomes in a PEX8-dependent manner and is found in purified peroxisomal matrix extracts. Supporting Evidence: PMID:10381339 Yor180Cp targeted GFP to peroxisomes in a PEX8-dependent manner PMID:10381339 Yor180Cp was also detected by mass spectrometric analysis of an HPLC-separated extract of yeast peroxisomal matrix proteins |
| GO:0005777 peroxisome | EXP PMID:10455114 Alternatives to the isomerase-dependent pathway for the beta... | ACCEPT | Summary: Gurvitz et al. 1999 identified DCI1 as encoding the peroxisomal di-isomerase; peroxisomal localisation is part of the characterisation in this paper (UniProt cites it for subcellular location). Supporting Evidence: PMID:10455114 Identification of YOR180c/DCI1 encoding peroxisomal delta(3,5)-delta(2,4)-dienoyl-CoA isomerase |
| GO:0005777 peroxisome | EXP PMID:10639339 Evidence for a novel pathway for the targeting of a Saccharo... | ACCEPT | Summary: Karpichev and Small 2000 showed Dci1p (and Eci1p) localise to peroxisomes, via a targeting route independent of the PTS1 and PTS2 receptors. Supporting Evidence: PMID:10639339 Both of these proteins are localized to peroxisomes |
| GO:0005777 peroxisome | IEA GO_REF:0000120 | ACCEPT | Summary: IEA (ARBA/UniProt subcellular location SL-0204) for peroxisome; consistent with the experimental data for Dci1p. Supporting Evidence: file:yeast/DCI1/DCI1-uniprot.txt SUBCELLULAR LOCATION: Peroxisome |
| GO:0005782 peroxisomal matrix | IBA GO_REF:0000033 | ACCEPT | Summary: IBA for peroxisomal matrix from the PANTHER ECI node; consistent with the yeast data (matrix proteomics) and with mammalian ECI2. Supporting Evidence: PMID:10381339 Yor180Cp was also detected by mass spectrometric analysis of an HPLC-separated extract of yeast peroxisomal matrix proteins |
| GO:0005782 peroxisomal matrix | IDA PMID:10381339 Preliminary characterization of Yor180Cp: identification of ... | ACCEPT | Summary: IDA: Dci1p was detected by mass spectrometry in HPLC-separated peroxisomal matrix protein extracts. Supporting Evidence: PMID:10381339 Yor180Cp was also detected by mass spectrometric analysis of an HPLC-separated extract of yeast peroxisomal matrix proteins |
| GO:0005829 cytosol | RCA GO_REF:0000123 | REMOVE | Summary: YeastPathways RCA from YEAST-FAO-PWY places the fatty acid oxidation pathway in the cytosol. Yeast beta-oxidation is exclusively peroxisomal and Dci1p is a peroxisomal matrix enzyme; the cytosol location is an artefact of the pathway-to-GO-CAM conversion. Supporting Evidence: PMID:10381339 Yor180Cp targeted GFP to peroxisomes in a PEX8-dependent manner PMID:10381339 Yor180Cp was also detected by mass spectrometric analysis of an HPLC-separated extract of yeast peroxisomal matrix proteins |
| GO:0006635 fatty acid beta-oxidation | IBA GO_REF:0000033 | ACCEPT | Summary: IBA for fatty acid beta-oxidation from the ECI family node. Dci1p acts in the auxiliary branch of beta-oxidation of unsaturated fatty acids (di-isomerase-dependent route), even though that route is dispensable for growth on oleate. Supporting Evidence: file:yeast/DCI1/DCI1-uniprot.txt Peroxisomal di-isomerase that is involved in fatty acid metabolism enzyme by converting 3,5-dienoyl-CoAs to the corresponding 2,4-dienoyl-CoAs |
| GO:0006635 fatty acid beta-oxidation | IEA GO_REF:0000041 | ACCEPT | Summary: IEA from the UniPathway mapping (UPA00659, fatty acid beta-oxidation); consistent with the experimentally characterised di-isomerase activity. Supporting Evidence: file:yeast/DCI1/DCI1-uniprot.txt PATHWAY: Lipid metabolism; fatty acid beta-oxidation |
| GO:0006635 fatty acid beta-oxidation | IMP PMID:10381339 Preliminary characterization of Yor180Cp: identification of ... | ACCEPT | Summary: IMP from Geisbrecht et al. 1999: yor180c deletion caused a mild but significant growth defect on oleic acid, indicating a role in fatty acid metabolism. Gurvitz et al. found no growth defect of dci1 on oleate, so the in vivo contribution is minor, but Dci1p catalyses a beta-oxidation step and the term is appropriate. Supporting Evidence: PMID:10381339 deletion of YOR180C from the yeast genome resulted in a mild but significant growth defect on oleic acid PMID:10455114 A strain devoid of Dci1p grew on oleic acid to wild-type levels |
| GO:0019395 fatty acid oxidation | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA for fatty acid oxidation (YEAST-FAO-PWY). Correct parent of fatty acid beta-oxidation, the process in which Dci1p's di-isomerase step operates. Supporting Evidence: file:yeast/DCI1/DCI1-uniprot.txt Peroxisomal di-isomerase that is involved in fatty acid metabolism enzyme by converting 3,5-dienoyl-CoAs to the corresponding 2,4-dienoyl-CoAs |
| GO:0051750 delta(3,5)-delta(2,4)-dienoyl-CoA isomerase activity | EXP PMID:10455114 Alternatives to the isomerase-dependent pathway for the beta... | UNDECIDED | Summary: Gurvitz et al. 1999 measured Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase activity (6 nmol/min/mg) in extracts of Dci1p-overproducing cells with 3,5,8,11,14-eicosapentenoyl-CoA as substrate. Ntamack et al. 2009 (PMID:19830908) found no di-isomerase activity in purified MBP-Yor180c fusion protein and a fourfold higher activity in yor180c deletion cells, and concluded that DCI1 does not encode the di-isomerase. Reason: Two experimental studies on the yeast protein disagree. The positive result used crude extracts of overproducing cells; the negative result used purified fusion protein and the deletion strain. The annotation is neither confirmed nor safely removable without resolving the conflict. Supporting Evidence: PMID:19830908 Moreover, the purified Yor180c protein fused to MBP did not exhibit any dienoyl-CoA isomerase activity. PMID:19830908 Dienoyl-CoA isomerase activity was very low in wild-type cells, fourfold higher in the YOR180c mutant, and not associated with purified Yor180c protein. PMID:10455114 Enzyme assays conducted on soluble extracts derived from yeast cells overproducing Dci1p using 3,5,8,11,14-eicosapentenoyl-CoA as substrate demonstrated a specific di-isomerase activity of 6 nmol x min(-1) per mg of protein |
| GO:0051750 delta(3,5)-delta(2,4)-dienoyl-CoA isomerase activity | IEA GO_REF:0000120 | UNDECIDED | Summary: IEA from Rhea (RHEA:45240) / EC 5.3.3.21 mapping of the UniProt catalytic activity, which is itself based on Gurvitz et al. 1999. The activity is disputed by Ntamack et al. 2009, so this row follows the experimental row. Reason: Rests on the same contested experimental claim as the EXP row. Supporting Evidence: PMID:19830908 The evidence obtained in this study supports the conclusion that the Yor180c protein is not a dienoyl-CoA isomerase. file:yeast/DCI1/DCI1-uniprot.txt Reaction=a (3E,5Z)-dienoyl-CoA = a (2E,4E)-(5,6-saturated)-dienoyl-CoA |
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Download this section (compressed HTML)Q: Is Dci1p a Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase? Extracts of overproducing cells had di-isomerase activity (PMID:10455114), but purified MBP-Dci1p had none and dci1 deletion raised cellular activity (PMID:19830908).
Q: Under which fatty acid diets (e.g. odd-position polyunsaturated fatty acids such as eicosapentaenoic or linoleic acid derivatives) does the Dci1p di-isomerase route carry significant flux in vivo?
Q: Does Dci1p form a stable hetero-oligomer with Eci1p in the peroxisomal matrix (piggy-back import), and does this complex alter either enzyme's activity?
Experiment: Assay untagged Dci1p purified from yeast and from E. coli, with Eci1p as a positive control, on 3,5-dienoyl-CoA substrates, and measure the activity in dci1, eci1 and dci1 eci1 extracts to locate the cellular di-isomerase activity.
Hypothesis: Dci1p itself catalyses the delta(3,5)-delta(2,4)-dienoyl-CoA isomerization.
Experiment: Compare 14C-labelled oleate and petroselinate/eicosapentaenoate oxidation and acyl-CoA intermediate profiles (LC-MS/MS) in wild type, dci1, eci1, sps19 and double mutants.
Hypothesis: Dci1p contributes measurably to beta-oxidation of fatty acids with double bonds at odd positions when the Eci1p route is limiting.
Peroxisomal protein; identification as a delta(3,5)-delta(2,4)-dienoyl-CoA isomerase involved in fatty acid metabolism is disputed; DCI1 has a paralog, ECI1, that arose from the whole genome duplication
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